NCBI Taxonomy: a comprehensive update on curation, resources and tools

Database, Год журнала: 2020, Номер 2020

Опубликована: Янв. 1, 2020

Abstract The National Center for Biotechnology Information (NCBI) Taxonomy includes organism names and classifications every sequence in the nucleotide protein databases of International Nucleotide Sequence Database Collaboration. Since last review this resource 2012, it has undergone several improvements. Most notable is shift from a single SQL database to series linked tied framework data called NameBank. This means that relations among elements can be adjusted more detail, resulting expanded annotation synonyms, ability flag with specific nomenclatural properties, enhanced tracking publications improved scientific authorities types. Additionally, practices utilized by NCBI curators major taxonomic groups are described, terms peculiar explained, external resources acknowledged updates tools other documented. URL: https://www.ncbi.nlm.nih.gov/taxonomy

Язык: Английский

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Trichoderma: The Current Status of Its Application in Agriculture for the Biocontrol of Fungal Phytopathogens and Stimulation of Plant Growth

International Journal of Molecular Sciences, Год журнала: 2022, Номер 23(4), С. 2329 - 2329

Опубликована: Фев. 19, 2022

Rhizosphere filamentous fungi of the genus Trichoderma, a dominant component various soil ecosystem mycobiomes, are characterized by ability to colonize plant roots. Detailed knowledge properties including metabolic activity and type interaction with plants other microorganisms, can ensure its effective use in agriculture. The growing interest application Trichoderma results from their direct indirect biocontrol potential against wide range phytopathogens. They act through complex mechanisms, such as mycoparasitism, degradation pathogen cell walls, competition for nutrients space, induction resistance. With constant exposure variety pathogens, especially fungi, increased resistance pathogens chemical pesticides, main challenge is develop biological protection alternatives. Among non-pathogenic seems be best candidate green technologies due biofertilization biostimulatory potential. Most species belong growth-promoting that produce phytohormones 1-aminocyclopropane-1-carboxylate (ACC) deaminase enzyme. In present review, current status gathered, which relevant growth stimulation fungal

Язык: Английский

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Fungal diversity notes 929–1035: taxonomic and phylogenetic contributions on genera and species of fungi

Fungal Diversity, Год журнала: 2019, Номер 95(1), С. 1 - 273

Опубликована: Март 1, 2019

This article is the ninth in series of Fungal Diversity Notes, where 107 taxa distributed three phyla, nine classes, 31 orders and 57 families are described illustrated. Taxa present study include 12 new genera, 74 species, combinations, two reference specimens, a re-circumscription epitype, 15 records sexual-asexual morph connections, hosts geographical distributions. Twelve genera comprise Brunneofusispora, Brunneomurispora, Liua, Lonicericola, Neoeutypella, Paratrimmatostroma, Parazalerion, Proliferophorum, Pseudoastrosphaeriellopsis, Septomelanconiella, Velebitea Vicosamyces. Seventy-four species Agaricus memnonius, A. langensis, Aleurodiscus patagonicus, Amanita flavoalba, subtropicana, Amphisphaeria mangrovei, Baorangia major, Bartalinia kunmingensis, Brunneofusispora sinensis, Brunneomurispora lonicerae, Capronia camelliae-yunnanensis, Clavulina thindii, Coniochaeta simbalensis, Conlarium thailandense, Coprinus trigonosporus, Liua muriformis, Cyphellophora filicis, Cytospora ulmicola, Dacrymyces invisibilis, Dictyocheirospora metroxylonis, Distoseptispora thysanolaenae, Emericellopsis koreana, Galiicola baoshanensis, Hygrocybe lucida, Hypoxylon teeravasati, Hyweljonesia indica, Keissleriella caraganae, Lactarius olivaceopallidus, Lactifluus midnapurensis, Lembosia brigadeirensis, Leptosphaeria urticae, Lonicericola hyaloseptispora, Lophiotrema mucilaginosis, Marasmiellus bicoloripes, Marasmius indojasminodorus, Micropeltis phetchaburiensis, Mucor orantomantidis, Murilentithecium Neobambusicola brunnea, Neoeutypella Neoroussoella heveae, Neosetophoma Ophiobolus malleolus, Parabambusicola Paratrimmatostroma Parazalerion Penicillium dokdoense, Peroneutypa Phaeosphaeria cycadis, Phanerochaete australosanguinea, Plectosphaerella Plenodomus artemisiae, P. lijiangensis, Proliferophorum thailandicum, Pseudoastrosphaeriellopsis kaveriana, Pseudohelicomyces menglunicus, Pseudoplagiostoma mangiferae, Robillarda Roussoella elaeicola, Russula choptae, R. uttarakhandia, Septomelanconiella thailandica, Spencermartinsia acericola, Sphaerellopsis isthmospora, Thozetella lithocarpi, Trechispora echinospora, Tremellochaete atlantica, Trichoderma koreanum, T. pinicola, rugulosum, chrysotexta, Vicosamyces venturisporus, Wojnowiciella kunmingensis Zopfiella indica. Three combinations rufomaculata, Lanmaoa pallidorosea rosicola. The specimens Canalisporium kenyense Tamsiniella labiosa designated. epitype Sarcopeziza sicula re-circumscribed based on cyto- histochemical analyses. connection sinensis reported from ferns Cirsium for first time. In addition, host country altipes, melleialba, Amarenomyces dactylidis, Chaetosphaeria panamensis, Coniella vitis, Coprinopsis kubickae, Dothiorella sarmentorum, Leptobacillium leptobactrum var. calidus, Muyocopron solani, Periconia cortaderiae, Phragmocamarosporium hederae, paraphysata Sphaeropsis eucalypticola.

Язык: Английский

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Antimicrobial Peptides: An Update on Classifications and Databases

International Journal of Molecular Sciences, Год журнала: 2021, Номер 22(21), С. 11691 - 11691

Опубликована: Окт. 28, 2021

Antimicrobial peptides (AMPs) are distributed across all kingdoms of life and an indispensable component host defenses. They consist predominantly short cationic with a wide variety structures targets. Given the ever-emerging resistance various pathogens to existing antimicrobial therapies, AMPs have recently attracted extensive interest as potential therapeutic agents. As discovery new has increased, many databases specializing in been developed collect both fundamental pharmacological information. In this review, we summarize sources, structures, modes action, classifications AMPs. Additionally, examine current AMP databases, compare valuable computational tools used predict activity mechanisms highlight machine learning approaches that can be employed improve combat global resistance.

Язык: Английский

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In honor of John Bissett: authoritative guidelines on molecular identification of Trichoderma

Fungal Diversity, Год журнала: 2021, Номер 107(1), С. 1 - 69

Опубликована: Фев. 5, 2021

Abstract Modern taxonomy has developed towards the establishment of global authoritative lists species that assume standardized principles recognition, at least in a given taxonomic group. However, fungi, delimitation is frequently subjective because it depends on choice concept and criteria selected by taxonomist. Contrary to it, identification fungal expected be accurate precise should predict properties are required for applications or relevant pathology. The industrial plant-beneficial fungi from genus Trichoderma (Hypocreales) offer suitable model address this collision between identification. A few decades ago, diversity was limited dozen species. introduction molecular evolutionary methods resulted exponential expansion taxonomy, with up 50 new recognized per year. Here, we have reviewed genus-wide compiled complete inventory all DNA barcoding material deposited public databases (the available website International Subcommission Taxonomy www.trichoderma.info ). Among 375 valid names as July 2020, 361 (96%) been cultivated vitro barcoded. Thus, protocol requires analysis three barcodes (ITS, tef1 , rpb2 ), supported online tools www.trichokey.info . We then used whole-genome sequenced (WGS) strains provide versatile practical examples identification, reveal shortcomings, discuss possible ambiguities. Based example, study shows why an intricate laborious task background mycology, biological skills, training analysis, knowledge literature. in-depth discussion concepts applied conclude these particularly implementation polyphasic approach first introduced John Bissett (1948–2020), whose work inspired current study. also propose regulatory unifying role international commissions particular groups. An important outcome demonstration urgent need cooperation researchers get prepared efficient use upcoming wave genomic data.

Язык: Английский

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Trichoderma Species: Our Best Fungal Allies in the Biocontrol of Plant Diseases—A Review

Plants, Год журнала: 2023, Номер 12(3), С. 432 - 432

Опубликована: Янв. 17, 2023

Biocontrol agents (BCA) have been an important tool in agriculture to prevent crop losses due plant pathogens infections and increase food production globally, diminishing the necessity for chemical pesticides fertilizers offering a more sustainable environmentally friendly option. Fungi from genus Trichoderma are among most used studied microorganisms as BCA variety of biocontrol traits, such parasitism, antibiosis, secondary metabolites (SM) production, defense system induction. Several species well-known mycoparasites. However, some those can antagonize other organisms nematodes pests, making this fungus very versatile BCA. has part innovative bioformulations, either just or combination with plant-beneficial microbes, growth-promoting bacteria (PGPB). Here, we review recent literature regarding studies about six species, T. atroviride, harzianum, asperellum, virens, longibrachiatum, viride, highlighting their traits use these fungal genera Trichoderma-based formulations control diseases, importance substitute fertilizers.

Язык: Английский

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Massive lateral transfer of genes encoding plant cell wall-degrading enzymes to the mycoparasitic fungus Trichoderma from its plant-associated hosts

PLoS Genetics, Год журнала: 2018, Номер 14(4), С. e1007322 - e1007322

Опубликована: Апрель 9, 2018

Unlike most other fungi, molds of the genus Trichoderma (Hypocreales, Ascomycota) are aggressive parasites fungi and efficient decomposers plant biomass. Although nutritional shifts common among hypocrealean there no examples such broad substrate versatility as that observed in Trichoderma. A phylogenomic analysis 23 (including nine spp. related Escovopsis weberi) revealed has evolved from an ancestor with limited cellulolytic capability fed on either or arthropods. The evolutionary genes encoding cell wall-degrading carbohydrate-active enzymes auxiliary proteins (pcwdCAZome, 122 gene families) based a tree / species reconciliation demonstrated formation was accompanied by unprecedented extent lateral transfer (LGT). Nearly one-half pcwdCAZome (41%) were obtained via LGT plant-associated filamentous belonging to different classes Ascomycota, while potential donors. In addition ability feed unrelated (such Basidiomycota), we also showed is capable endoparasitism range including extant This phenomenon not E. weberi rarely mycoparasitic fungi. Thus, our study suggests linked parasitize taxonomically (up adelphoparasitism strict sense). may have allowed primarily mycotrophic evolve into

Язык: Английский

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Mechanisms for plant growth promotion activated by Trichoderma in natural and managed terrestrial ecosystem

Microbiological Research, Год журнала: 2024, Номер 281, С. 127621 - 127621

Опубликована: Янв. 21, 2024

Язык: Английский

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Trichoderma afroharzianum TRI07 metabolites inhibit Alternaria alternata growth and induce tomato defense-related enzymes

Scientific Reports, Год журнала: 2024, Номер 14(1)

Опубликована: Янв. 22, 2024

Abstract Identifying a viable substitute for the limited array of current antifungal agents stands as crucial objective in modern agriculture. Consequently, extensive worldwide research has been undertaken to unveil eco-friendly and effective capable controlling pathogens resistant presently employed fungicides. This study explores efficacy Trichoderma isolates combating tomato leaf spot disease, primarily caused by Alternaria alternata . The identified pathogen, A. Alt3, was isolated confirmed through ITS region (OQ888806). Six were assessed their ability inhibit Alt3 hyphal growth using dual culture, ethyl acetate extract, volatile organic compounds (VOCs) techniques. most promising biocontrol isolate T. afroharzianum TRI07 based on three markers: (OQ820171), translation elongation factor alpha 1 gene (OR125580), RNA polymerase II subunit (OR125581). extract subjected GC–MS analysis, revealing spathulenol, triacetin, aspartame main compounds, with percentages 28.90, 14.03, 12.97%, respectively. Analysis TRI07-VOCs solid-phase microextraction technique indicated that abundant included ethanol, hydroperoxide, 1-methylhexyl, 1-octen-3-one. When interacted 34 identified, major components including 1-octen-3-one, hexanedioic acid, bis(2-ethylhexyl) ester. In greenhouse experiment, treatment 48 h before inoculation (A3 treatment) resulted reduction disease severity (16.66%) incidence (44.44%). Furthermore, A3 led improved performance parameters increased chlorophyll content. After 21 days post-inoculation, associated production antioxidant enzymes (CAT, POD, SOD, PPO), while infected plants exhibited elevated levels oxidative stress markers MDA H 2 O HPLC analysis extracts from revealed higher phenolic acids such gallic, chlorogenic, caffeic, syringic, coumaric acids, well flavonoid catechin, rutin, vanillin. novelty lies bridging gap between strain-specific attributes practical application, enhancing understanding TRI07’s potential integrated pest management. concludes presents natural biological activity, effectively promoting plant growth. findings have implications agriculture, suggesting sustainable strategy can enhance crop resilience contribute management practices.

Язык: Английский

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Taxonomic and phylogenetic contributions to fungi associated with the invasive weed Chromolaena odorata (Siam weed)

Fungal Diversity, Год журнала: 2020, Номер 101(1), С. 1 - 175

Опубликована: Март 1, 2020

Язык: Английский

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